|
| Status |
Public on Nov 21, 2017 |
| Title |
2G-mono |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow (femurs and tibias)
|
| Organism |
Mus musculus |
| Characteristics |
strain: Wild-type C57BL/6 mice (CD45.2)
tissue: bone marrow
cell type: GMP-derived Ly6Chi monocytes
differentiation: In vitro
gating/cell markers: c-Kit- CD11b+ Ly6G- CD115+ Ly6Chi F4/80-
|
| Extracted molecule |
total RNA |
| Extraction protocol |
GMPs and MDPs were isolated from the pooled bone marrow of 20 mice and cultured in vitro in media (RPMI with 10% FCS and 1% penicillin-streptomycin) supplemented with M-CSF (50 ng/ml; Peprotech). On days 2, 3 and 4 of culture, cells were harvested and FACS sorted for monocyte progenitors (Ly6G− CD11b− c-Kit+ Ly6C+ CD115+) and Ly6Chi monocytes (Ly6G− CD11b+ c-Kit− Ly6Chi CD115+ F4/80−). Whole cell lysates of cells isolated at the three timepoints were pooled for each cell type, and RNA was extracted from using an RNeasy mini kit (Qiagen).
Each sample was subjected to library preparation with a KAPA kit (Kapa Biosystems) and multiplexed across 4 lanes to yield a mean of 32.9 million 75 bp single-end reads per sample (standard deviation 1.7 million reads).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
GMP-derived Ly6Chi monocytes
|
| Data processing |
RNA-Seq was aligned with STAR-2.5.1b to mm10 with gencode vM4 gene models
bams were passed through a picard pipeline of CleanSam, Sort, and MarkDups
Reads were counted with featureCounts from Rsubread version 1.22 against gencode vM4 gene models
Genes that had at least 1 cpm in at least 2 samples were retained for normalization via TMM limma/voom pipeline
Genome_build: mm10
Supplementary_files_format_and_content: count_matrix.txt contains read counts from featureCounts. Rows are genes, columns are samples.
|
| |
|
| Submission date |
Oct 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Helen S Goodridge |
| E-mail(s) |
Helen.Goodridge@csmc.edu
|
| Organization name |
Cedars-Sinai Medical Center
|
| Street address |
8700 Beverly Boulevard
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90048 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE88982 |
RNA-seq of mouse myeloid progenitors reveals two independent pathways for monocyte production via GMPs and MDPs |
|
| Relations |
| BioSample |
SAMN05930271 |
| SRA |
SRX2254699 |
